Alignment of IL_44465.1 sequences from 3D to the JAR3D model

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The correspondence between sequences from 3D structures and the motif group is shown in blue and the JAR3D alignment of the sequences to the motif group is shown in black. Occasionally the two disagree, in which case the JAR3D alignment is shown in red.
Column number:
Node in JAR3D model:
Insertion positions indicated by I:
Position in motif group:		1
1
I

2
2

1
3
2
I

4
3

2
5
4
I

6
7

3
7
7
I

8
8


9
7
I

10
7

4
11
6
I

12
5

5
13
2
I

14
2

6
15
1
I


In
acceptance
region

Cutoff
score
Full
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distance
Interior
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Alignment
score
deficit
IL_44465.1_Instance_1 IL_44465.1,IL_1SI2_002,U403_A405UGAUGA
IL_44465.1_Sequence_1 IL_44465.11SI2_U403_A405UGA*UGAtrue100000.00
IL_44465.1_Instance_2 IL_44465.1,IL_1SI3_001,U403_A405UGAUGA
IL_44465.1_Sequence_2 IL_44465.11SI3_U403_A405UGA*UGAtrue100000.00
IL_44465.1_Instance_3 IL_44465.1,IL_8P9A_408,C686_G648CGGCGG
IL_44465.1_Sequence_3 IL_44465.18P9A_C686_G648CGG*CGGtrue97000.29
IL_44465.1_Instance_4 IL_44465.1,IL_8P9A_384,U150_A164UGUAGA
IL_44465.1_Sequence_4 IL_44465.18P9A_U150_A164UGU*AGAtrue98000.22
IL_44465.1_Instance_5 IL_44465.1,IL_5UNE_001,U39_A9UGGUGA
IL_44465.1_Sequence_5 IL_44465.15UNE_U39_A9UGG*UGAtrue94000.55
IL_44465.1_Instance_6 IL_44465.1,IL_7LYF_002,C84_G48CAAUGG
IL_44465.1_Sequence_6 IL_44465.17LYF_C84_G48CAA*UGGtrue89001.09
IL_44465.1_Instance_7 IL_44465.1,IL_5UNE_009,U39_A9UGGUGA
IL_44465.1_Sequence_7 IL_44465.15UNE_U39_A9UGG*UGAtrue94000.55
IL_44465.1_Instance_8 IL_44465.1,IL_7ZO1_011,G16_C5GUAUUC
IL_44465.1_Sequence_8 IL_44465.17ZO1_G16_C5GUA*UUCtrue65003.34
IL_44465.1_Instance_9 IL_44465.1,IL_9DFE_023,G931_C846GGAGCGC
IL_44465.1_Sequence_9 IL_44465.19DFE_G931_C846GGAG*CGCtrue58003.98

Conserved interactions between motif group positions in IL_44465.1:
1 2 s35 
1 6 cWW 
2 3 s35 
2 6 s55 
3 4 cWW 
3 5 s55 
4 5 s35 
5 6 s35
JAR3D SCFG/MRF model for IL_44465.1:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [6] // Initial node
BasepairNode | Deletion Probability [0.0000132986348294] | Pair Probability [[0.008704022,0.016892921,0.009736844,0.185266315,0.000000000],[0.019232100,0.009115905,0.206431280,0.011372198,0.000000000],[0.009746898,0.205120396,0.001931795,0.022427573,0.000000000],[0.235350996,0.011023681,0.038152472,0.009494606,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.883805084,0.115305590,0.000858659,0.000030666] | Left Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair U403 - A405 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.227272727,0.045454545,0.590909091,0.136363636,0.000000000] | Position [1] | Left Index [2] | Right Index [5] // Fixed node on left for 1SI2|1|B|G|404
InitialNode  | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [5] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.045454545,0.045454545,0.772727273,0.136363636,0.000000000] | Position [2] | Left Index [3] | Right Index [5] // Fixed node on right for 1SI2|1|B|G|404||||4_675
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [4] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010118179,0.076931961,0.010436126,0.201455731,0.000000000],[0.015986981,0.009651137,0.151030962,0.011214610,0.000000000],[0.010340726,0.172458588,0.002170614,0.115910039,0.000000000],[0.160891733,0.011804496,0.022985109,0.016613008,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [4] // Basepair A405 - U403 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node type *
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncation
Sequences of instances from IL_44465.1:
> IL_44465.1  1SI2 U  403 A  405
UGA*UGA
> IL_44465.1  1SI3 U  403 A  405
UGA*UGA
> IL_44465.1  8P9A C  686 G  648
CGG*CGG
> IL_44465.1  8P9A U  150 A  164
UGU*AGA
> IL_44465.1  5UNE U   39 A    9
UGG*UGA
> IL_44465.1  7LYF C   84 G   48
CAA*UGG
> IL_44465.1  5UNE U   39 A    9
UGG*UGA
> IL_44465.1  7ZO1 G   16 C    5
GUA*UUC
> IL_44465.1  9DFE G  931 C  846
GGAG*CGC